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Complete genome sequence of Flavobacteriaceae strain KCTC 52651 isolated from seawater recirculating aquaculture system

해수 순환여과양식시스템에서 분리된 Flavobacteriaceae 균주 KCTC 52651의 유전체 분석

Kim, Young-Sam;Jeon, Young Jae;Kim, Kyoung-Ho
김영삼;전용재;김경호

  • Received : 2019.05.02
  • Accepted : 2019.05.07
  • Published : 2019.06.30

Abstract

A novel bacterium, designated strain RR4-38 (= KCTC 52651 = DSM 108068), belonging to the family Flavobacteriaceae was isolated from a biofilter in the seawater recirculating aquaculture system in South Korea. A single complete genome contig which is 3,182,272 bp with 41.9% G+C content was generated using PacBio RS II platform. The genome includes 2,829 protein-coding genes, 6 rRNA genes, 38 tRNA genes, 4 non-coding RNA genes, and 9 pseudogenes. The results will provide insights for understanding microbial activity in the seawater recirculating aquaculture system.

Keywords

Flavobacteriaceae;complete genome;seawater recirculating aquaculture system

References

  1. Grant JR, Arantes AS, and Stothard P. 2012. Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics 13, 202. https://doi.org/10.1186/1471-2164-13-202
  2. Grissa I, Vergnaud G, Pourcel C, Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P, et al. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35, W52-W57. https://doi.org/10.1093/nar/gkm360
  3. Sandu S and Hallerm E. 2013. Biodegradation of nitrogen in a commercial recirculating aquaculture facility, In Biodegradation - Engineering and technology. InTechOpen Limited, London, UK.
  4. Verreth JAJ, Eding EH, Martins CIM, Blancheton JP, Heinsbroek LTN, d'Orbcastel ER, Schneider O, and Verdegem MCJ. 2010. New developments in recirculating aquaculture systems in Europe: A perspective on environmental sustainability. Aquacult. Eng. 43, 83-93. https://doi.org/10.1016/j.aquaeng.2010.09.002
  5. Wilke A, Zagnitko O, Formsma K, Aziz RK, Kubal M, Vonstein V, Stevens R, McNeil LK, Edwards RA, Pusch GD, et al. 2008. The RAST server: Rapid annotations using subsystems technology. BMC Genomics 9, 75. https://doi.org/10.1186/1471-2164-9-75
  6. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, and Wishart DS. 2016. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 44, W16-W21. https://doi.org/10.1093/nar/gkw387
  7. Bregnballe J. 2015. A guide to recirculation aquaculture. FAO.
  8. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, et al. 2013. Nonhybrid, finished microbial genome assemblies from longread SMRT sequencing data. Nat. Methods 10, 563-569. https://doi.org/10.1038/nmeth.2474
  9. DiCuccio M, Zaslavsky L, Chetvernin V, Ostell J, Badretdin A, Tatusova T, Lomsadze A, Borodovsky M, Nawrocki EP, and Pruitt KD. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.

Acknowledgement

Supported by : Pukyong National University